Blender Cycles Lightmap Baking
Yea, I face similar trouble, but all that I have now - the combined texture is a gives you the best image. But you also can try to bake Ambient Occlusion, and add it with a combination of Color ramp - so maybe it gives you the correct result. But I'm sure that when you convert it on a gtlf format, It's not saving as ambient occlusion "slot" for material - ambient becomes a part of a texture. You can see it clearly on three.js editor - on material props, and read an answer on 
Ambient occlusion in Principled BSDF